Project on Type 2 diabetic and Hyperglycemic Pancreatic Islets

Introduction

Type 2 Diabetes (T2D) is a serious health concern and identifying gene markers associated with the disease can help catch it early in new patients.

Our analysis is focused on

  • Identifying gene markers

  • Identifying key over- and under-expressed genes

Looking into co-expression of key genes

Data source:

A Systems Genetics Approach Identifies Genes and Pathways for Type 2 Diabetes in Human Islets
(PMID: 22768844) (GEO ID: GDS4337)

Materials - Data Set Description

Data set overview:

  • 14481 different genes

  • 63 samples

    • 9 with T2D

    • 54 controls

Descriptive statistics:

  • Similar mean gene expression across groups

  • Overall low mean expression levels

  • Slightly right-skewed distribution

  • => Investigate significant difference of genes between the groups

Materials - Wrangling

Frederik

Methods - Median Expression Differences

Goal: Identify genes with largest expression differences between T2D and control


Workflow:

  1. Compute median expression per gene for T2D and Control

  2. Calculate absolute differences between group medians per gene

  3. Rank genes by largest absolute difference

  4. Visualize top genes:

    • Bar plot of top 30 genes (median differences)
    • Boxplots of sample-level expression variation for top 10 genes

Methods - p.value

  1. Transform data

  2. Pivot Longer

  3. Nest the Log Fold Changes

  4. Creating linear regression models for each gene

    • lm(log_fold_change ~ disease.state)

  5. Select genes from significant p-values

Results - Median Expression Differences

Per gene:

  • T2D: 9 samples

  • Control: 54 samples

Results - p.value

  • Final p-value selection was p < 0.01
  • - 635 genes labelled significant
  • Top 30 most significant (lowest p-vals) chosen for visualisation

Results - combined / correlation matrix

Discussion

1) Difference in two methods

2) Sum up which genes are found by the analysis

3) does they support the litterature? uniprot…

Conclusion